Back-Translation for Discovering Distant Protein Homologies

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Back-Translation for Discovering Distant Protein Homologies
Background: Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins’ common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. Results: We developed a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. Our implementation is freely available at Conclusions: Our a...
Marta Gîrdea, Laurent Noé, Gregory Ku
Added 25 May 2010
Updated 25 May 2010
Type Conference
Year 2009
Where WABI
Authors Marta Gîrdea, Laurent Noé, Gregory Kucherov
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